PROJECT SUMMARY Autoimmune thyroid diseases (AITD) frequently develop together with type 1 diabetes (T1D), a combination considered a variant of the Autoimmune Polyglandular Syndrome type 3 (APS3v). Our goals are to identify the joint susceptibility genes for AITD+T1D (APS3v), to dissect the mechanisms by which they cause disease, and to translate this knowledge into new therapies. In the last grant cycle we made substantial progress toward these goals: (1) We mapped new susceptibility genes/loci for APS3v using whole genome approaches; (2) We discovered a unique HLA-DR-pocket signature critical for the development of APS3v; (3) We identified 4 pathogenic thyroid & islet peptides that bind to the APS3v-specific HLA-DR & activate T-cells; (4) We identified genetic-epigenetic interactions that trigger AITD & T1D; (5) We discovered a compound, Cepharanthine, that blocks thyroglobulin peptide presentation & prevents autoimmune thyroiditis in mice. Building on these findings we propose to: (1) Sequence 3 APS3v loci we mapped to identify rare variants predisposing to APS3v; and (2) Translate our discovery of the APS3v-DR pocket into new therapies by blocking this pocket. Our hypothesis is that in addition to common variants, rare non-HLA variants are also critical to the joint etiology of AITD+T1D, and that identifying them will reveal new mechanisms & therapeutic targets; furthermore, we hypothesize that binding of pathogenic peptides to the APS3v-DR pocket & their presentation to T-cells triggers APS3v, and that blocking pathogenic peptide binding to HLA-DR can be used to treat or prevent APS3v. Our specific aims are: Specific Aim 1: Identifying rare variants in 3 loci (2q, 8p, Xp) that are linked with APS3v using targeted next generation sequencing (NGS) in our unique dataset of families in which AITD+T1D cluster. Identified variants that are predicted to alter gene function will be replicated in 2 large cohorts of APS3v patients and families. Specific Aim 2: Screening of a large library for small molecule inhibitors (SMI's) that block pathogenic peptide binding to the APS3v-DR pocket to identify hits. Hit SMI's will be confirmed in vitro, ex vivo and in vivo. Lead SMI's will be optimized by medicinal chemistry to improve potency, selectivity, & pharmacokinetic properties. Specific Aim 3: Designing D-amino acid peptide blockers of pathogenic peptide binding to the APS3v HLA-DR pocket. We will design in silico D-amino acid peptides (D-peptides) predicted to block binding and presentation of pathogenic thyroid/islet peptides. Predicted D-peptide blockers will be confirmed in vitro, ex vivo, and in vivo. In summary, our multidisciplinary translational project builds on the knowledge gained in the last grant period. Our goals are to continue our successful gene discovery using targeted NGS of mapped APS3v loci to identify new therapeutic targets, and to pursue pre-clinical development of novel therapies for APS3v by blocking the APS3v-DR pocket we identified. The strength of our therapeutic approach is that it is both selective as only T- cells recognizing pathogenic peptides are targeted and personalized since only patients carrying the APS3v- DR will be treated. Our studies will hopefully lead to new therapies for APS3v, as well as for AITD and T1D.